1qw8: Difference between revisions

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-[[Image:1qw8.jpg|left|200px]]
- {{Structure
+==Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with Ara-alpha(1,3)-Xyl==
-|PDB= 1qw8 |SIZE=350|CAPTION= <scene name='initialview01'>1qw8</scene>, resolution 1.80&Aring;
+<StructureSection load='1qw8' size='340' side='right'caption='[[1qw8]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=KHO:4-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-TETRAHYDRO-PYRAN-2,3,5-TRIOL'>KHO</scene>
+<table><tr><td colspan='2'>[[1qw8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QW8 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-N-arabinofuranosidase Alpha-N-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-|GENE= ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qw8 OCA], [https://pdbe.org/1qw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qw8 RCSB], [https://www.ebi.ac.uk/pdbsum/1qw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qw8 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1pz3|1PZ3]], [[1pz2|1PZ2]], [[1qw9|1QW9]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qw8 OCA], [http://www.ebi.ac.uk/pdbsum/1qw8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qw8 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/IABF_GEOSE IABF_GEOSE] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref> <ref>PMID:7887599</ref>
+== Evolutionary Conservation ==
-'''Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with Ara-alpha(1,3)-Xyl'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qw/1qw8_consurf.spt"</scriptWhenChecked>
-High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-QW8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW8 OCA].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qw8 ConSurf].
+<div style="clear:both"></div>
-==Reference==
+== References ==
-Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase., Hovel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D, EMBO J. 2003 Oct 1;22(19):4922-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14517232 14517232]
+<references/>
-[[Category: Alpha-N-arabinofuranosidase]]
+__TOC__
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bassov, T.]]
+[[Category: Bassov T]]
-[[Category: Belakhov, V.]]
+[[Category: Belakhov V]]
-[[Category: Hoevel, K.]]
+[[Category: Hoevel K]]
-[[Category: Niefind, K.]]
+[[Category: Niefind K]]
-[[Category: Schomburg, D.]]
+[[Category: Schomburg D]]
-[[Category: Shallom, D.]]
+[[Category: Shallom D]]
-[[Category: Shoham, G.]]
+[[Category: Shoham G]]
-[[Category: Shoham, Y.]]
+[[Category: Shoham Y]]
-[[Category: hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:19:57 2008''